<?xml version="1.0" ?>
<tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction" version="2018.4">
	<description> - Beta diversity rarefaction</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  qiime diversity beta-rarefaction --i-table=$itable
  
  #def list_dict_to_string(list_dict):
  	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
  	#for d in list_dict[1:]:
  		#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
  	#end for
  	#return $file_list
  #end def
  
   --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-clustering-method=$pclusteringmethod --p-metric=$pmetric --p-sampling-depth="$psamplingdepth"
   
  #if str($pcorrelationmethod) != 'None':
   --p-correlation-method=$pcorrelationmethod
  #end if
  
  #if str($pcolorscheme) != 'None':
   --p-color-scheme=$pcolorscheme
  #end if
  
   --o-visualization=ovisualization
   
  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
  #if str($iphylogeny) != 'None':
   --i-phylogeny=$iphylogeny
  #end if
  
  #if $piterations:
   --p-iterations=$piterations
  #end if
  ;
  qiime tools export ovisualization.qzv --output-dir out   && mkdir -p '$ovisualization.files_path'
  && cp -r out/* '$ovisualization.files_path'
  && mv '$ovisualization.files_path/index.html' '$ovisualization';
  ]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table upon which to perform beta diversity rarefaction analyses.  [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics]  [optional]" name="iphylogeny" optional="True" type="data"/>

		<param label="--p-metric: The beta diversity metric to be computed.
                                  [required]" name="pmetric" optional="False" type="select">
			<option value="hamming">hamming</option>
			<option value="sqeuclidean">sqeuclidean</option>
			<option value="cityblock">cityblock</option>
			<option value="sokalmichener">sokalmichener</option>
			<option value="braycurtis">braycurtis</option>
			<option value="cosine">cosine</option>
			<option value="euclidean">euclidean</option>
			<option value="rogerstanimoto">rogerstanimoto</option>
			<option value="weighted_unifrac">weighted_unifrac</option>
			<option value="canberra">canberra</option>
			<option value="seuclidean">seuclidean</option>
			<option value="correlation">correlation</option>
			<option value="unweighted_unifrac">unweighted_unifrac</option>
			<option value="sokalsneath">sokalsneath</option>
			<option value="chebyshev">chebyshev</option>
			<option value="mahalanobis">mahalanobis</option>
			<option value="matching">matching</option>
			<option value="kulsinski">kulsinski</option>
			<option value="yule">yule</option>
			<option value="dice">dice</option>
			<option value="russellrao">russellrao</option>
			<option value="wminkowski">wminkowski</option>
			<option value="jaccard">jaccard</option>
		</param>
		<param label="--p-clustering-method: Samples can be clustered with neighbor
                                  joining or UPGMA. An arbitrary rarefaction
                                  trial will be used for the tree, and the
                                  remaining trials are used to calculate the
                                  support of the internal nodes of that tree.
                                  [required]" name="pclusteringmethod" optional="False" type="select">
			<option value="upgma">upgma</option>
			<option value="nj">nj</option>
		</param>

		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata used for the Emperor jackknifed PCoA plot.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

		<param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing the diversity metric.  [required]" name="psamplingdepth" optional="False" type="text"/>
		<param label="--p-iterations: Number of times to rarefy the feature table at a given sampling depth.  [default: 10]" name="piterations" optional="True" type="integer" value="10"/>

		<param label="--p-correlation-method: The Mantel correlation test to be applied
                                  when computing correlation between beta
                                  diversity distance matrices.  [default:
                                  spearman]" name="pcorrelationmethod" optional="True" type="select">			
			<option selected="True" value="spearman">spearman</option>
			<option value="pearson">pearson</option>
		</param>

		<param label="--p-color-scheme: The matplotlib color scheme to generate the
                                  heatmap with.  [default: BrBG]" name="pcolorscheme" optional="True" type="select">			
			<option value="PiYG">PiYG</option>
			<option value="RdYlGn_r">RdYlGn_r</option>
			<option value="RdYlBu_r">RdYlBu_r</option>
			<option value="RdYlGn">RdYlGn</option>
			<option value="BrBG_r">BrBG_r</option>
			<option value="RdYlBu">RdYlBu</option>
			<option value="RdGy">RdGy</option>
			<option value="PuOr">PuOr</option>
			<option value="RdBu_r">RdBu_r</option>
			<option value="RdGy_r">RdGy_r</option>
			<option value="PiYG_r">PiYG_r</option>
			<option value="RdBu">RdBu</option>
			<option value="PuOr_r">PuOr_r</option>
			<option value="PRGn">PRGn</option>
			<option selected="True" value="BrBG">BrBG</option>
			<option value="PRGn_r">PRGn_r</option>
		</param>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Beta diversity rarefaction
--------------------------

Repeatedly rarefy a feature table to compare beta diversity results within
a given rarefaction depth.  For a given beta diversity metric, this
visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
by UPGMA or neighbor joining with support calculation, and a heatmap
showing the correlation between rarefaction trials of that beta diversity
metric.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table upon which to perform beta diversity rarefaction
    analyses.
phylogeny : Phylogeny[Rooted], optional
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree. [required for phylogenetic metrics]
metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'unweighted_unifrac', 'weighted_unifrac', 'wminkowski', 'yule'})
    The beta diversity metric to be computed.
clustering_method : Str % Choices({'nj', 'upgma'})
    Samples can be clustered with neighbor joining or UPGMA. An arbitrary
    rarefaction trial will be used for the tree, and the remaining trials
    are used to calculate the support of the internal nodes of that tree.
metadata : Metadata
    The sample metadata used for the Emperor jackknifed PCoA plot.
sampling_depth : Int % Range(1, None)
    The total frequency that each sample should be rarefied to prior to
    computing the diversity metric.
iterations : Int % Range(2, None), optional
    Number of times to rarefy the feature table at a given sampling depth.
correlation_method : Str % Choices({'pearson', 'spearman'}), optional
    The Mantel correlation test to be applied when computing correlation
    between beta diversity distance matrices.
color_scheme : Str % Choices({'BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r', 'PuOr', 'PuOr_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r'}), optional
    The matplotlib color scheme to generate the heatmap with.

Returns
-------
visualization : Visualization
		\
    ]]>
	</help>
</tool>